[Freesurfer] Error from mri_glmfit-sim - Input volume voxel dimensions do not match

s: tkmedit fsaverage orig.mgz -aseg -overlay study1.glmdir/group_diff/sig.mgh -fminmax 0.1 5 5. Correction (mri_glmfit-sim) breaks. mri_glmfit-sim --glmdir study1.glmdir --grf 1.3 neg --cwpvalthresh .05 Full error below, any help would be appreciated! Freesurfer 5.3 running on Mac OS X 10.9.x Peter

[Freesurfer] Job: Postdoc in Cognitive Neuroscience at UConn

University of Connecticut College of Liberal Arts and Sciences Postdoctoral Fellow in Cognitive Neuroscience The University of Connecticut’s new Brain Imaging Research Center (BIRC) invites The BIRC is a 3,200 square foot, research-dedicated imaging facility housing a research-dedicated 3T Siem

[Freesurfer] Postdoctoral position in Cognitive Neuroscience and Reading Disability

Postdoctoral position in Cognitive Neuroscience and Reading Disability Haskins Laboratories (PI: Dr. Julie A. Van Dyke), New Haven, CT Application deadline: April 15, 2013 Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants shou

[Freesurfer] Job: Research Associate in Cognitive Neuroscience

Job Announcement – March 2013 Research Associate Haskins Laboratories, 300 George Street, Suite 900, New Haven CT 06511 Project Directors: Dr. Kenneth Pugh, Dr. Jay Rueckl Haskins Laboratories is seeking a Research Associate for projects related to Cognitive Neuroscience and Language/Reading Dev

[Freesurfer] Job: Postdoc in Cognitive Neuroscience at Haskins Laboratories

Postdoctoral position in Cognitive Neuroscience at Haskins Laboratories Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a Ph.D. in psychology, linguistics, cognitive neuroscience, or a related field. The selected

[Freesurfer] Mac OS X 10.8.5 breaks recon-all

I updated my Mac OS X install to 10.8.5 late yesterday and now recon-all (FS 5.3) fails early in the processing pipeline (Talairach). I've attempted running the process with both my own data that works on Freesurfer 5.3 with 10.8.4 and receive the same error message. I have two identical comp

Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all

ase > on the machine running 10.8.4? I will update my Mac tonight to the most > recent version of OSX and attempt to duplicate the issue. I will keep you > updated. > > -Zeke > > On 09/17/2013 12:57 PM, Peter J. Molfese wrote: >> I updated my Mac OS X install to 10.8.

Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all

(using homebrew)? Other than installing XQuartz, freesurfer should run on a > clean system. > > -Zeke > > On 09/17/2013 02:53 PM, Peter J. Molfese wrote: >> The DYLD message does not appear on the 10.8.4 system. Both systems have >> homebrew (http://brew.sh) installe

[Freesurfer] mri_cvs_register error on Mac

All, I've been trying to use mri_cvs_register on a 64-bit mac and received the following error (below). Google found a couple of hits that others are having this problem but no solution. I'm running the most recent version from version 5.1 with the patch on the release notes page ($Id: mri_cv

Re: [Freesurfer] Recent paper on FreeSurfer reliability

We run things on an Xgrid cluster that is now a mixture of Macs running Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from asegstats2table and aparcstats2table are identical after running 100 subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also ran a few

[Freesurfer] DTI Paramters

ny for DTI specifically. Also, any idea when version 5.1 will be out of beta? Thanks, Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molf...@yale.edu ___ Freesurfer ma

[Freesurfer] FreesurferEnv and matlab directory creation

empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molf...@yal

Re: [Freesurfer] mri_cvs_register update

Is this significant enough that we should re-run data processed using the standard recon-all stream in version 5.1? Thanks, Peter On Jun 10, 2011, at 3:28 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT) > From: Lilla Zollei > Subject

[Freesurfer] Pulvinar Segmentation

Hi, I'm interested in pulling out segmentation stats on the Pulvinar. I noticed that Pulvinar is listed in the FreeSurferColorLUT.txt but isn't in the aseg.stats. Is there a way to get segmentation information for the Pulvinar? best, Peter ___ Fre

Re: [Freesurfer] error during mri_cvs_register

Is there a reason that the Mac binaries are not available in 64-bit versions? On Jun 21, 2011, at 3:11 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Date: Tue, 21 Jun 2011 21:11:54 +0200 > From: Martin Kavec > Subject: Re: [Freesurfer] error during mri_cvs_register > To: David Brang > Cc:

Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects

A script is definitely the easiest way to process quite a few subjects. You can save some headache by using a recon-all command with an input for your image files. For example: "recon-all -s sleep_001 -i sleep_001.nii -all" will create a subject folder in the correct location named sleep_001 a

[Freesurfer] trac-all "Error: bvecs and bvals don't have the same number of entries"

but when I attempted to add "export LC_ALL=en_US", the problem persists. I have looked in the files and found that they do indeed have different numbers of entries. The scans were performed on a Siemens TimTrio 3T scanner. Is there something else I should set? Peter J. Molfese

Re: [Freesurfer] trac-all "Error: bvecs and bvals don't have the same number of entries"

bval files to be 3 column and 1 column format respectively. 3. run trac-all -prep with a config file showing where the dicom images are and hand specifying the bvec and bval files Peter Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven